Commit 5f142911 authored by Nicolas  MAILLET's avatar Nicolas MAILLET
Browse files

Modify input -e and -m (replace -e 2 -e 3 by -e 2 3)

parent e4519749
...@@ -16,7 +16,7 @@ You can obtain help by using: ...@@ -16,7 +16,7 @@ You can obtain help by using:
.. code-block:: none .. code-block:: none
rpg -\\-help rpg --help
Installation Installation
...@@ -35,7 +35,7 @@ Then you can use: ...@@ -35,7 +35,7 @@ Then you can use:
.. code-block:: none .. code-block:: none
rpg -\\-help rpg --help
From source code From source code
---------------- ----------------
...@@ -113,7 +113,7 @@ To perform sequential digestion of the sequence "QWSDORESDF" with enzymes 2 and ...@@ -113,7 +113,7 @@ To perform sequential digestion of the sequence "QWSDORESDF" with enzymes 2 and
.. code-block:: none .. code-block:: none
rpg -i QWSDORESDF -o output_file.fasta -e 2 -e 5 rpg -i QWSDORESDF -o output_file.fasta -e 2 5
Sequential digestion of a (multi)fasta file Sequential digestion of a (multi)fasta file
""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""
...@@ -122,7 +122,7 @@ To perform sequential digestion of `input_file.fasta` with enzymes 2 and 5 and s ...@@ -122,7 +122,7 @@ To perform sequential digestion of `input_file.fasta` with enzymes 2 and 5 and s
.. code-block:: none .. code-block:: none
rpg -i input_file.fasta -o output_file.fasta -e 2 -e 5 rpg -i input_file.fasta -o output_file.fasta -e 2 5
Concurrent digestion of a (multi)fasta file Concurrent digestion of a (multi)fasta file
""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""
...@@ -131,7 +131,7 @@ To perform concurrent digestion of `input_file.fasta` with enzymes 2 and 5 and s ...@@ -131,7 +131,7 @@ To perform concurrent digestion of `input_file.fasta` with enzymes 2 and 5 and s
.. code-block:: none .. code-block:: none
rpg -i input_file.fasta -o output_file.fasta -e 2 -e 5 -d c rpg -i input_file.fasta -o output_file.fasta -e 2 5 -d c
Adding a new enzyme Adding a new enzyme
------------------- -------------------
...@@ -156,7 +156,7 @@ Here are all available options in **RPG**: ...@@ -156,7 +156,7 @@ Here are all available options in **RPG**:
**-d, -\\-digest**: Digestion mode. Either 's', 'sequential', 'c' or 'concurrent' (default: s). See :ref:`digestion` for more information. **-d, -\\-digest**: Digestion mode. Either 's', 'sequential', 'c' or 'concurrent' (default: s). See :ref:`digestion` for more information.
**-e, -\\-enzymes**: Enzyme(s) id number to use (*i.e.* -e 0 -e 5 -e 10 to use enzymes 0, 5 and 10). Use -l first to get enzyme ids. See :ref:`enzymes` for more information. **-e, -\\-enzymes**: Enzyme(s) id number to use (*i.e.* -e 0 5 10 to use enzymes 0, 5 and 10). Use -l first to get enzyme ids. See :ref:`enzymes` for more information.
**-f, -\\-fmt**: Output file format. Either 'fasta', 'csv', or 'tsv' (default: fasta). See :ref:`formats` for more information. **-f, -\\-fmt**: Output file format. Either 'fasta', 'csv', or 'tsv' (default: fasta). See :ref:`formats` for more information.
...@@ -164,7 +164,7 @@ Here are all available options in **RPG**: ...@@ -164,7 +164,7 @@ Here are all available options in **RPG**:
**-l, -\\-list**: Display the list of available enzymes. **-l, -\\-list**: Display the list of available enzymes.
**-m, -\\-miscleavage**: Percentage of miscleavage, between 0 and 100, by enzyme(s). It should be in the same order as the -\\-enzymes options (*i.e.* -m 15 -m 5 -m 10). It works only for sequential digestion (default: 0). See :ref:`miscleavage` for more information. **-m, -\\-miscleavage**: Percentage of miscleavage, between 0 and 100, by enzyme(s). It should be in the same order as the -\\-enzymes options (*i.e.* -m 15 5.2 10). It works only for sequential digestion (default: 0). See :ref:`miscleavage` for more information.
**-n, -\\-noninteractive**: Non-interactive mode. No standard output, only error(s) (-\\-quiet enable, overwrite -v). If output filename already exists, output file will be overwritten. See :ref:`nointer` for more information. **-n, -\\-noninteractive**: Non-interactive mode. No standard output, only error(s) (-\\-quiet enable, overwrite -v). If output filename already exists, output file will be overwritten. See :ref:`nointer` for more information.
...@@ -192,7 +192,7 @@ Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after ...@@ -192,7 +192,7 @@ Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after
.. code-block:: none .. code-block:: none
$ rpg -i PKPKPKPK -e 28 -e 29 $ rpg -i PKPKPKPK -e 28 29
>Input_0_afterP_1_1_115.13198_5.54 >Input_0_afterP_1_1_115.13198_5.54
P P
>Input_1_afterP_3_2_243.30608_9.4 >Input_1_afterP_3_2_243.30608_9.4
...@@ -212,7 +212,7 @@ Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the follow ...@@ -212,7 +212,7 @@ Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the follow
.. code-block:: none .. code-block:: none
$ rpg -i PKPKPKPK -e 28 -e 29 -d c $ rpg -i PKPKPKPK -e 28 29 -d c
>Input_0_afterP-afterK_1_1_115.13198_5.54 >Input_0_afterP-afterK_1_1_115.13198_5.54
P P
>Input_1_afterP-afterK_2_1_146.18938_9.4 >Input_1_afterP-afterK_2_1_146.18938_9.4
...@@ -246,7 +246,7 @@ For example, using: ...@@ -246,7 +246,7 @@ For example, using:
.. code-block:: none .. code-block:: none
rpg -i QWSDORESDF -e 1 -e 2 -e 3 -m 1.4 -m 2.6 rpg -i QWSDORESDF -e 1 2 3 -m 1.4 2.6
will assign a miscleavage probability of `1.4%` to enzyme `1`, a miscleavage probability of `2.6%` to enzyme `2` and a miscleavage probability of `0%` to enzyme `3` (default behavior). For enzyme `1`, each cleavage will then have a probability of 0.014 to **not** occur. will assign a miscleavage probability of `1.4%` to enzyme `1`, a miscleavage probability of `2.6%` to enzyme `2` and a miscleavage probability of `0%` to enzyme `3` (default behavior). For enzyme `1`, each cleavage will then have a probability of 0.014 to **not** occur.
......
...@@ -39,7 +39,7 @@ import os ...@@ -39,7 +39,7 @@ import os
import sys import sys
import uuid import uuid
from pathlib import Path from pathlib import Path
#from context import rpg from context import rpg
from rpg import core from rpg import core
from rpg import digest from rpg import digest
from rpg import enzyme from rpg import enzyme
...@@ -177,12 +177,12 @@ def get_enzymes_to_use(mode, id_enz_selected, miscleavage): ...@@ -177,12 +177,12 @@ def get_enzymes_to_use(mode, id_enz_selected, miscleavage):
# Ask user to give correct enzymes ids # Ask user to give correct enzymes ids
while not enzymes_to_use: while not enzymes_to_use:
id_enz_inp = input("Choose which enzyme(s) to use, separated by" id_enz_inp = input("Choose which enzyme(s) to use, separated by"
" comma (example: 1,5,6). (q) to quit:\n") " space (example: 1 5 6). (q) to quit:\n")
# Quit # Quit
if "q" in id_enz_inp: if "q" in id_enz_inp:
sys.exit(0) sys.exit(0)
# Get a list of ids # Get a list of ids
for i in id_enz_inp.split(","): for i in id_enz_inp.split(" "):
try: try:
# Convert it to int # Convert it to int
i = int(i) i = int(i)
...@@ -195,11 +195,11 @@ def get_enzymes_to_use(mode, id_enz_selected, miscleavage): ...@@ -195,11 +195,11 @@ def get_enzymes_to_use(mode, id_enz_selected, miscleavage):
mc_enz_inputed = [] mc_enz_inputed = []
if mode == "sequential": if mode == "sequential":
mc_enz_inp = input("Percentage of miscleavage per inputed" mc_enz_inp = input("Percentage of miscleavage per inputed"
" enzyme (default 0), separated by comma" " enzyme (default 0), separated by sapce"
" (example: 1,5,6):\n") " (example: 1.2 5 6):\n")
if mc_enz_inp: if mc_enz_inp:
# Get a list of int # Get a list of int
for i in mc_enz_inp.split(","): for i in mc_enz_inp.split(" "):
try: try:
# Convert it to int # Convert it to int
i = float(i) i = float(i)
...@@ -252,10 +252,9 @@ def main(): ...@@ -252,10 +252,9 @@ def main():
default="s", help="Digestion mode. Either 's', 'seque" default="s", help="Digestion mode. Either 's', 'seque"
"ntial', 'c' or 'concurrent' (default: s)") "ntial', 'c' or 'concurrent' (default: s)")
parser.add_argument("-e", "--enzymes", metavar="", default=[], parser.add_argument("-e", "--enzymes", metavar="", default=[],
action='append', type=restricted_enzyme_id, nargs='+', type=restricted_enzyme_id,
help="Id of enzyme(s) to use (i.e. -e 0 -e 5 -e 10 to" help="Id of enzyme(s) to use (i.e. -e 0 5 10 to use "
" use enzymes 0, 5 and 10). Use -l first to get " "enzymes 0, 5 and 10). Use -l first to get enzyme ids")
"enzyme ids")
parser.add_argument("-f", "--fmt", metavar="", parser.add_argument("-f", "--fmt", metavar="",
choices=['fasta', 'csv', 'tsv'], default="fasta", choices=['fasta', 'csv', 'tsv'], default="fasta",
help="Output file format. Either 'fasta', 'csv', or " help="Output file format. Either 'fasta', 'csv', or "
...@@ -266,11 +265,11 @@ def main(): ...@@ -266,11 +265,11 @@ def main():
group_launch.add_argument("-l", "--list", action="store_true", group_launch.add_argument("-l", "--list", action="store_true",
help="Display the list of available enzymes") help="Display the list of available enzymes")
parser.add_argument("-m", "--miscleavage", metavar="", default=[], parser.add_argument("-m", "--miscleavage", metavar="", default=[],
action='append', type=restricted_float, nargs='+', type=restricted_float,
help="Percentage of miscleavage, between 0 and 100," help="Percentage of miscleavage, between 0 and 100,"
" by enzyme(s). It should be in the same order than " " by enzyme(s). It should be in the same order than "
"-enzymes options (i.e. -m 15 -m 5 -m 10). Only for " "-enzymes options (i.e. -m 15 5 10). Only for sequenti"
"sequential digestion (default: 0)") "al digestion (default: 0)")
parser.add_argument("-n", "--noninteractive", action='store_true', parser.add_argument("-n", "--noninteractive", action='store_true',
help="Non-interactive mode. No standard output, only " help="Non-interactive mode. No standard output, only "
"error(s) (--quiet enable, overwrite -v). If output " "error(s) (--quiet enable, overwrite -v). If output "
......
...@@ -85,12 +85,12 @@ def test_output_results(capsys, tmpdir): ...@@ -85,12 +85,12 @@ def test_output_results(capsys, tmpdir):
assert out == output_file.read() assert out == output_file.read()
assert output_file.read() == "Original_header,No_peptide,Enzyme,Cleaving_"\ assert output_file.read() == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\ "pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.52598,3.6,WQSD"\ "Input,0,fake_enzyme1,4,4,534.52598,3.14,WQSD"\
"\nInput,1,fake_enzyme1,7,3,349.29758,3.4,ES"\ "\nInput,1,fake_enzyme1,7,3,349.29758,3.04,ES"\
"D\nInput,2,fake_enzyme1,12,5,495.48938,3.6,"\ "D\nInput,2,fake_enzyme1,12,5,495.48938,3.14,"\
"FZQSD\nInput,3,fake_enzyme1,15,3,349.29758,"\ "FZQSD\nInput,3,fake_enzyme1,15,3,349.29758,"\
"3.4,ESD\nInput,4,fake_enzyme1,16,1,165.1918"\ "3.04,ESD\nInput,4,fake_enzyme1,16,1,165.1918"\
"8,5.54,F\n" "8,5.97,F\n"
# TSV output # TSV output
output_file = tmpdir.join("test_result.tsv") output_file = tmpdir.join("test_result.tsv")
...@@ -103,12 +103,12 @@ def test_output_results(capsys, tmpdir): ...@@ -103,12 +103,12 @@ def test_output_results(capsys, tmpdir):
assert output_file.read() == "Original_header\tNo_peptide\tEnzyme\tCleavi"\ assert output_file.read() == "Original_header\tNo_peptide\tEnzyme\tCleavi"\
"ng_pos\tPeptide_size\tPeptide_mass\tpI\tSeq"\ "ng_pos\tPeptide_size\tPeptide_mass\tpI\tSeq"\
"uence\nInput\t0\tfake_enzyme1\t4\t4\t534.52"\ "uence\nInput\t0\tfake_enzyme1\t4\t4\t534.52"\
"598\t3.6\tWQSD\nInput\t1\tfake_enzyme1\t7\t"\ "598\t3.14\tWQSD\nInput\t1\tfake_enzyme1\t7\t"\
"3\t349.29758\t3.4\tESD\nInput\t2\tfake_enzy"\ "3\t349.29758\t3.04\tESD\nInput\t2\tfake_enzy"\
"me1\t12\t5\t495.48938\t3.6\tFZQSD\nInput\t3"\ "me1\t12\t5\t495.48938\t3.14\tFZQSD\nInput\t3"\
"\tfake_enzyme1\t15\t3\t349.29758\t3.4\tESD"\ "\tfake_enzyme1\t15\t3\t349.29758\t3.04\tESD"\
"\nInput\t4\tfake_enzyme1\t16\t1\t165.19188"\ "\nInput\t4\tfake_enzyme1\t16\t1\t165.19188"\
"\t5.54\tF\n" "\t5.97\tF\n"
# Fasta output # Fasta output
output_file = tmpdir.join("test_result.fasta") output_file = tmpdir.join("test_result.fasta")
...@@ -118,12 +118,12 @@ def test_output_results(capsys, tmpdir): ...@@ -118,12 +118,12 @@ def test_output_results(capsys, tmpdir):
core.output_results(str(output_file), all_seq_digested, fmt, quiet, verbose) core.output_results(str(output_file), all_seq_digested, fmt, quiet, verbose)
out, err = capsys.readouterr() out, err = capsys.readouterr()
assert out == output_file.read() assert out == output_file.read()
assert output_file.read() == ">Input_0_fake_enzyme1_4_4_534.52598_3.6\nWQ"\ assert output_file.read() == ">Input_0_fake_enzyme1_4_4_534.52598_3.14\nWQ"\
"SD\n>Input_1_fake_enzyme1_7_3_349.29758_3.4"\ "SD\n>Input_1_fake_enzyme1_7_3_349.29758_3.04"\
"\nESD\n>Input_2_fake_enzyme1_12_5_495.48938"\ "\nESD\n>Input_2_fake_enzyme1_12_5_495.48938"\
"_3.6\nFZQSD\n>Input_3_fake_enzyme1_15_3_349"\ "_3.14\nFZQSD\n>Input_3_fake_enzyme1_15_3_349"\
".29758_3.4\nESD\n>Input_4_fake_enzyme1_16_1"\ ".29758_3.04\nESD\n>Input_4_fake_enzyme1_16_1"\
"_165.19188_5.54\nF\n" "_165.19188_5.97\nF\n"
# CSV output in quiet # CSV output in quiet
seq = "WQSDESDFZQSDESDF" seq = "WQSDESDFZQSDESDF"
...@@ -139,12 +139,12 @@ def test_output_results(capsys, tmpdir): ...@@ -139,12 +139,12 @@ def test_output_results(capsys, tmpdir):
assert out == "" assert out == ""
assert output_file.read() == "Original_header,No_peptide,Enzyme,Cleaving_"\ assert output_file.read() == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\ "pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.52598,3.6,WQSD"\ "Input,0,fake_enzyme1,4,4,534.52598,3.14,WQSD"\
"\nInput,1,fake_enzyme1,7,3,349.29758,3.4,ES"\ "\nInput,1,fake_enzyme1,7,3,349.29758,3.04,ES"\
"D\nInput,2,fake_enzyme1,12,5,495.48938,3.6,"\ "D\nInput,2,fake_enzyme1,12,5,495.48938,3.14,"\
"FZQSD\nInput,3,fake_enzyme1,15,3,349.29758,"\ "FZQSD\nInput,3,fake_enzyme1,15,3,349.29758,"\
"3.4,ESD\nInput,4,fake_enzyme1,16,1,165.1918"\ "3.04,ESD\nInput,4,fake_enzyme1,16,1,165.1918"\
"8,5.54,F\n" "8,5.97,F\n"
# CSV output in verbose > 2 # CSV output in verbose > 2
seq = "WQSDESDFZQSDESDF" seq = "WQSDESDFZQSDESDF"
...@@ -158,12 +158,12 @@ def test_output_results(capsys, tmpdir): ...@@ -158,12 +158,12 @@ def test_output_results(capsys, tmpdir):
out, err = capsys.readouterr() out, err = capsys.readouterr()
assert output_file.read() == "Original_header,No_peptide,Enzyme,Cleaving_"\ assert output_file.read() == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\ "pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.52598,3.6,WQSD"\ "Input,0,fake_enzyme1,4,4,534.52598,3.14,WQSD"\
"\nInput,1,fake_enzyme1,7,3,349.29758,3.4,ES"\ "\nInput,1,fake_enzyme1,7,3,349.29758,3.04,ES"\
"D\nInput,2,fake_enzyme1,12,5,495.48938,3.6,"\ "D\nInput,2,fake_enzyme1,12,5,495.48938,3.14,"\
"FZQSD\nInput,3,fake_enzyme1,15,3,349.29758,"\ "FZQSD\nInput,3,fake_enzyme1,15,3,349.29758,"\
"3.4,ESD\nInput,4,fake_enzyme1,16,1,165.1918"\ "3.04,ESD\nInput,4,fake_enzyme1,16,1,165.1918"\
"8,5.54,F\n" "8,5.97,F\n"
# Verbose > 2 # Verbose > 2
assert out == "\nNumber of cleavage: 4\nCleavage position: 4, 7, 12, 15\n"\ assert out == "\nNumber of cleavage: 4\nCleavage position: 4, 7, 12, 15\n"\
"Number of miscleavage: 0\nmiscleavage position: \nmis"\ "Number of miscleavage: 0\nmiscleavage position: \nmis"\
...@@ -181,7 +181,7 @@ def test_peptide(): ...@@ -181,7 +181,7 @@ def test_peptide():
print_res = pep0.__repr__() print_res = pep0.__repr__()
assert print_res == "Original header: Test\nNo. peptide: 1\nEnzyme: fake_"\ assert print_res == "Original header: Test\nNo. peptide: 1\nEnzyme: fake_"\
"enzyme\nCleav. pos: 3\nPep. size: 8\nPep. mass: 1012"\ "enzyme\nCleav. pos: 3\nPep. size: 8\nPep. mass: 1012"\
".98488\nPep. pI: 3.29\nSequence: QWSDESDF\n" ".98488\nPep. pI: 2.91\nSequence: QWSDESDF\n"
# Test function '__eq__()' # Test function '__eq__()'
pep1 = sequence.Peptide(header, seq, enz_name, 1, 3) pep1 = sequence.Peptide(header, seq, enz_name, 1, 3)
...@@ -201,12 +201,12 @@ def test_peptide(): ...@@ -201,12 +201,12 @@ def test_peptide():
# Test function '__format__()' # Test function '__format__()'
format_res = pep0.__format__("csv") format_res = pep0.__format__("csv")
assert format_res == "Test,1,fake_enzyme,3,8,1012.98488,3.29,QWSDESDF" assert format_res == "Test,1,fake_enzyme,3,8,1012.98488,2.91,QWSDESDF"
format_res = pep2.__format__("tsv") format_res = pep2.__format__("tsv")
assert format_res == "Test\t1\tfake_enzyme\t2\t8\t1012.98488\t3.29\tQWSD"\ assert format_res == "Test\t1\tfake_enzyme\t2\t8\t1012.98488\t2.91\tQWSD"\
"ESDF" "ESDF"
format_res = pep3.__format__("fasta") format_res = pep3.__format__("fasta")
assert format_res == ">Test_2_fake_enzyme_3_8_1012.98488_3.29\nQWSDESDF" assert format_res == ">Test_2_fake_enzyme_3_8_1012.98488_2.91\nQWSDESDF"
# Test function 'def get_isoelectric_point():' # Test function 'def get_isoelectric_point():'
assert pep3.get_isoelectric_point() == 3.29 assert pep3.get_isoelectric_point() == 2.91
...@@ -26,10 +26,10 @@ def test_resultonedigestion(): ...@@ -26,10 +26,10 @@ def test_resultonedigestion():
"66\nPeptides: [Original header: Test\nNo. "\ "66\nPeptides: [Original header: Test\nNo. "\
"peptide: 0\nEnzyme: fake_enzyme\nCleav. po"\ "peptide: 0\nEnzyme: fake_enzyme\nCleav. po"\
"s: 3\nPep. size: 8\nPep. mass: 1012.98488"\ "s: 3\nPep. size: 8\nPep. mass: 1012.98488"\
"\nPep. pI: 3.29\nSequence: QWSDESDF\n, Ori"\ "\nPep. pI: 2.91\nSequence: QWSDESDF\n, Ori"\
"ginal header: Test\nNo. peptide: 1\nEnzyme"\ "ginal header: Test\nNo. peptide: 1\nEnzyme"\
": fake_enzyme\nCleav. pos: 4\nPep. size: 8"\ ": fake_enzyme\nCleav. pos: 4\nPep. size: 8"\
"\nPep. mass: 1012.98488\nPep. pI: 3.29\nSe"\ "\nPep. mass: 1012.98488\nPep. pI: 2.91\nSe"\
"quence: QWSDESDF\n]\n" "quence: QWSDESDF\n]\n"
# Test function '__eq__()' # Test function '__eq__()'
...@@ -53,15 +53,15 @@ def test_resultonedigestion(): ...@@ -53,15 +53,15 @@ def test_resultonedigestion():
# Test function '__format__()' # Test function '__format__()'
format_res = res_dig0.__format__("csv") format_res = res_dig0.__format__("csv")
assert format_res == "Test,0,fake_enzyme,3,8,1012.98488,3.29,QWSDESDF\nTe"\ assert format_res == "Test,0,fake_enzyme,3,8,1012.98488,2.91,QWSDESDF\nTe"\
"st,1,fake_enzyme,4,8,1012.98488,3.29,QWSDESDF\n" "st,1,fake_enzyme,4,8,1012.98488,2.91,QWSDESDF\n"
format_res = res_dig0.__format__("tsv") format_res = res_dig0.__format__("tsv")
assert format_res == "Test\t0\tfake_enzyme\t3\t8\t1012.98488\t3.29\tQWSDE"\ assert format_res == "Test\t0\tfake_enzyme\t3\t8\t1012.98488\t2.91\tQWSDE"\
"SDF\nTest\t1\tfake_enzyme\t4\t8\t1012.98488\t3.29\t"\ "SDF\nTest\t1\tfake_enzyme\t4\t8\t1012.98488\t2.91\t"\
"QWSDESDF\n" "QWSDESDF\n"
format_res = res_dig0.__format__("fasta") format_res = res_dig0.__format__("fasta")
assert format_res == ">Test_0_fake_enzyme_3_8_1012.98488_3.29\nQWSDESDF\n"\ assert format_res == ">Test_0_fake_enzyme_3_8_1012.98488_2.91\nQWSDESDF\n"\
">Test_1_fake_enzyme_4_8_1012.98488_3.29\nQWSDESDF\n" ">Test_1_fake_enzyme_4_8_1012.98488_2.91\nQWSDESDF\n"
# Test function 'pop_peptides()' # Test function 'pop_peptides()'
assert res_dig5.peptides != [] assert res_dig5.peptides != []
...@@ -350,21 +350,21 @@ def test_digest_from_input(capsys, tmpdir): ...@@ -350,21 +350,21 @@ def test_digest_from_input(capsys, tmpdir):
"[Original header: Input\nNo. peptide: 0"\ "[Original header: Input\nNo. peptide: 0"\
"\nEnzyme: fake_enzyme1\nCleav. pos: 4\nPe"\ "\nEnzyme: fake_enzyme1\nCleav. pos: 4\nPe"\
"p. size: 4\nPep. mass: 534.52598\nPep. pI"\ "p. size: 4\nPep. mass: 534.52598\nPep. pI"\
": 3.6\nSequence: WQSD\n, Original header:"\ ": 3.14\nSequence: WQSD\n, Original header:"\
" Input\nNo. peptide: 1\nEnzyme: fake_enzy"\ " Input\nNo. peptide: 1\nEnzyme: fake_enzy"\
"me1\nCleav. pos: 7\nPep. size: 3\nPep. ma"\ "me1\nCleav. pos: 7\nPep. size: 3\nPep. ma"\
"ss: 349.29758\nPep. pI: 3.4\nSequence: ES"\ "ss: 349.29758\nPep. pI: 3.04\nSequence: ES"\
"D\n, Original header: Input\nNo. peptide:"\ "D\n, Original header: Input\nNo. peptide:"\
" 2\nEnzyme: fake_enzyme1\nCleav. pos: 12"\ " 2\nEnzyme: fake_enzyme1\nCleav. pos: 12"\
"\nPep. size: 5\nPep. mass: 495.48938\nPep"\ "\nPep. size: 5\nPep. mass: 495.48938\nPep"\
". pI: 3.6\nSequence: FZQSD\n, Original he"\ ". pI: 3.14\nSequence: FZQSD\n, Original he"\
"ader: Input\nNo. peptide: 3\nEnzyme: fake"\ "ader: Input\nNo. peptide: 3\nEnzyme: fake"\
"_enzyme1\nCleav. pos: 15\nPep. size: 3\nP"\ "_enzyme1\nCleav. pos: 15\nPep. size: 3\nP"\
"ep. mass: 349.29758\nPep. pI: 3.4\nSequen"\ "ep. mass: 349.29758\nPep. pI: 3.04\nSequen"\
"ce: ESD\n, Original header: Input\nNo. pe"\ "ce: ESD\n, Original header: Input\nNo. pe"\
"ptide: 4\nEnzyme: fake_enzyme1\nCleav. po"\ "ptide: 4\nEnzyme: fake_enzyme1\nCleav. po"\
"s: 16\nPep. size: 1\nPep. mass: 165.19188"\ "s: 16\nPep. size: 1\nPep. mass: 165.19188"\
"\nPep. pI: 5.54\nSequence: F\n]\n" "\nPep. pI: 5.97\nSequence: F\n]\n"
# Test fasta file # Test fasta file
fasta_file = tmpdir.join("test.fasta") fasta_file = tmpdir.join("test.fasta")
...@@ -376,28 +376,28 @@ def test_digest_from_input(capsys, tmpdir): ...@@ -376,28 +376,28 @@ def test_digest_from_input(capsys, tmpdir):
"[Original header: Fake1\nNo. peptide: 0\n"\ "[Original header: Fake1\nNo. peptide: 0\n"\
"Enzyme: fake_enzyme1\nCleav. pos: 4\nPep."\ "Enzyme: fake_enzyme1\nCleav. pos: 4\nPep."\
" size: 4\nPep. mass: 534.52598\nPep. pI: "\ " size: 4\nPep. mass: 534.52598\nPep. pI: "\
"3.6\nSequence: WQSD\n, Original header: F"\ "3.14\nSequence: WQSD\n, Original header: F"\
"ake1\nNo. peptide: 1\nEnzyme: fake_enzyme"\ "ake1\nNo. peptide: 1\nEnzyme: fake_enzyme"\
"1\nCleav. pos: 7\nPep. size: 3\nPep. mass"\ "1\nCleav. pos: 7\nPep. size: 3\nPep. mass"\
": 349.29758\nPep. pI: 3.4\nSequence: ESD"\ ": 349.29758\nPep. pI: 3.04\nSequence: ESD"\
"\n, Original header: Fake1\nNo. peptide: "\ "\n, Original header: Fake1\nNo. peptide: "\
"2\nEnzyme: fake_enzyme1\nCleav. pos: 12\n"\ "2\nEnzyme: fake_enzyme1\nCleav. pos: 12\n"\
"Pep. size: 5\nPep. mass: 495.48938\nPep. "\ "Pep. size: 5\nPep. mass: 495.48938\nPep. "\
"pI: 3.6\nSequence: FZQSD\n, Original head"\ "pI: 3.14\nSequence: FZQSD\n, Original head"\
"er: Fake1\nNo. peptide: 3\nEnzyme: fake_e"\ "er: Fake1\nNo. peptide: 3\nEnzyme: fake_e"\
"nzyme1\nCleav. pos: 15\nPep. size: 3\nPep"\ "nzyme1\nCleav. pos: 15\nPep. size: 3\nPep"\
". mass: 349.29758\nPep. pI: 3.4\nSequence"\ ". mass: 349.29758\nPep. pI: 3.04\nSequence"\
": ESD\n, Original header: Fake1\nNo. pept"\ ": ESD\n, Original header: Fake1\nNo. pept"\
"ide: 4\nEnzyme: fake_enzyme1\nCleav. pos:"\ "ide: 4\nEnzyme: fake_enzyme1\nCleav. pos:"\
" 16\nPep. size: 1\nPep. mass: 165.19188\n"\ " 16\nPep. size: 1\nPep. mass: 165.19188\n"\
"Pep. pI: 5.54\nSequence: F\n]\n" "Pep. pI: 5.97\nSequence: F\n]\n"
assert res[1][0].__repr__() == "Number of cleavage: 0\nNumber of miscle"\ assert res[1][0].__repr__() == "Number of cleavage: 0\nNumber of miscle"\
"avage: 0\nPositions of miscleavage: []"\ "avage: 0\nPositions of miscleavage: []"\
"\nRatio of miscleavage: 0\nPeptides: [O"\ "\nRatio of miscleavage: 0\nPeptides: [O"\
"riginal header: Fake2\nNo. peptide: 0\nEn"\ "riginal header: Fake2\nNo. peptide: 0\nEn"\
"zyme: fake_enzyme1\nCleav. pos: 0\nPep. s"\ "zyme: fake_enzyme1\nCleav. pos: 0\nPep. s"\
"ize: 15\nPep. mass: 2014.35098\nPep. pI: "\ "ize: 15\nPep. mass: 2014.35098\nPep. pI: "\
"6.91\nSequence: NPHARDORCOMPLET\n]\n" "7.16\nSequence: NPHARDORCOMPLET\n]\n"
# Test fastq file (same result) # Test fastq file (same result)
fastq_file = tmpdir.join("test.fastq") fastq_file = tmpdir.join("test.fastq")
...@@ -410,25 +410,25 @@ def test_digest_from_input(capsys, tmpdir): ...@@ -410,25 +410,25 @@ def test_digest_from_input(capsys, tmpdir):
"[Original header: Fake1\nNo. peptide: 0\n"\ "[Original header: Fake1\nNo. peptide: 0\n"\
"Enzyme: fake_enzyme1\nCleav. pos: 4\nPep."\ "Enzyme: fake_enzyme1\nCleav. pos: 4\nPep."\
" size: 4\nPep. mass: 534.52598\nPep. pI: "\ " size: 4\nPep. mass: 534.52598\nPep. pI: "\
"3.6\nSequence: WQSD\n, Original header: F"\ "3.14\nSequence: WQSD\n, Original header: F"\
"ake1\nNo. peptide: 1\nEnzyme: fake_enzyme"\ "ake1\nNo. peptide: 1\nEnzyme: fake_enzyme"\
"1\nCleav. pos: 7\nPep. size: 3\nPep. mass"\ "1\nCleav. pos: 7\nPep. size: 3\nPep. mass"\
": 349.29758\nPep. pI: 3.4\nSequence: ESD"\ ": 349.29758\nPep. pI: 3.04\nSequence: ESD"\
"\n, Original header: Fake1\nNo. peptide: "\ "\n, Original header: Fake1\nNo. peptide: "\
"2\nEnzyme: fake_enzyme1\nCleav. pos: 12\n"\ "2\nEnzyme: fake_enzyme1\nCleav. pos: 12\n"\
"Pep. size: 5\nPep. mass: 495.48938\nPep. "\ "Pep. size: 5\nPep. mass: 495.48938\nPep. "\
"pI: 3.6\nSequence: FZQSD\n, Original head"\ "pI: 3.14\nSequence: FZQSD\n, Original head"\
"er: Fake1\nNo. peptide: 3\nEnzyme: fake_e"\ "er: Fake1\nNo. peptide: 3\nEnzyme: fake_e"\
"nzyme1\nCleav. pos: 15\nPep. size: 3\nPep"\ "nzyme1\nCleav. pos: 15\nPep. size: 3\nPep"\
". mass: 349.29758\nPep. pI: 3.4\nSequence"\ ". mass: 349.29758\nPep. pI: 3.04\nSequence"\
": ESD\n, Original header: Fake1\nNo. pept"\ ": ESD\n, Original header: Fake1\nNo. pept"\
"ide: 4\nEnzyme: fake_enzyme1\nCleav. pos:"\ "ide: 4\nEnzyme: fake_enzyme1\nCleav. pos:"\
" 16\nPep. size: 1\nPep. mass: 165.19188\n"\ " 16\nPep. size: 1\nPep. mass: 165.19188\n"\
"Pep. pI: 5.54\nSequence: F\n]\n" "Pep. pI: 5.97\nSequence: F\n]\n"
assert res[1][0].__repr__() == "Number of cleavage: 0\nNumber of miscle"\ assert res[1][0].__repr__() == "Number of cleavage: 0\nNumber of miscle"\
"avage: 0\nPositions of miscleavage: []"\ "avage: 0\nPositions of miscleavage: []"\
"\nRatio of miscleavage: 0\nPeptides: [O"\ "\nRatio of miscleavage: 0\nPeptides: [O"\
"riginal header: Fake2\nNo. peptide: 0\nEn"\ "riginal header: Fake2\nNo. peptide: 0\nEn"\
"zyme: fake_enzyme1\nCleav. pos: 0\nPep. s"\ "zyme: fake_enzyme1\nCleav. pos: 0\nPep. s"\
"ize: 15\nPep. mass: 2014.35098\nPep. pI: "\ "ize: 15\nPep. mass: 2014.35098\nPep. pI: "\
"6.91\nSequence: NPHARDORCOMPLET\n]\n" "7.16\nSequence: NPHARDORCOMPLET\n]\n"
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