Package this lib for pypi

Package this lib for pypi:

• Add command line
• Add pyproject.toml
• Add CI/CD
• Set up PyPI account for release
• Write README

#1

crisprbact/cli.py

-import click
 from crisprbact import on_target_predict
-from pathlib import Path
 from Bio import SeqIO
+import click
 
 
 class Config(object):
@@ -11,6 +10,8 @@ class Config(object):
 
 pass_config = click.make_pass_decorator(Config, ensure=True)
 
+HEADER = ["target", "PAM position", "prediction", "seq_id"]
+
 
 @click.group()
 @click.option("-v", "--verbose", is_flag=True)
@@ -31,19 +32,17 @@ def predict(config):
 @pass_config
 def from_str(config, target, output_file):
     """
-    Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target activity from a target gene.
+    Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target
+    activity from a target gene.
 
-    [OUTPUT_FILE] file where the precitions are saved. Default = "stdout"
+    [OUTPUT_FILE] file where the candidate guide RNAs are saved. Default = "stdout"
 
     """
     if config.verbose:
         print_parameters(target)
 
     guide_rnas = on_target_predict(target)
-    click.echo(
-        "\t".join(["target", "PAM position", "prediction", "input_id"]),
-        file=output_file,
-    )
+    click.echo("\t".join(HEADER), file=output_file)
     write_guide_rnas(guide_rnas, output_file)
 
 
@@ -51,24 +50,28 @@ def from_str(config, target, output_file):
 @click.option(
     "-t", "--target", type=click.File("rU"), required=True, help="Sequence file"
 )
-@click.option("-f", "--seq-format", help="Sequence file format", default="fasta")
+@click.option(
+    "-f",
+    "--seq-format",
+    type=click.Choice(["fasta", "fa", "gb", "genbank"]),
+    help="Sequence file format",
+    default="fasta",
+    show_default=True,
+)
 @click.argument("output-file", type=click.File("w"), default="-")
 @pass_config
 def from_seq(config, target, seq_format, output_file):
     """
-    Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target activity from a target gene.
+    Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target
+    activity from a target gene.
 
-    [OUTPUT_FILE] file where the precitions are saved. Default = "stdout"
+    [OUTPUT_FILE] file where the candidate guide RNAs are saved. Default = "stdout"
 
     """
     fg = "blue"
     if config.verbose:
         print_parameters(target.name, fg)
-    # with open(target, "rU") as handle:
-    click.echo(
-        "\t".join(["target", "PAM position", "prediction", "input_id"]),
-        file=output_file,
-    )
+    click.echo("\t".join(HEADER), file=output_file)
     for record in SeqIO.parse(target, seq_format):
         if config.verbose:
             click.secho(" - search guide RNAs for %s " % record.id, fg=fg)
@@ -81,7 +84,7 @@ def print_parameters(target, fg="blue"):
     click.secho("Target sequence : %s" % target, fg=fg)
 
 
-def write_guide_rnas(guide_rnas, output_file, input_id="N/A"):
+def write_guide_rnas(guide_rnas, output_file, seq_id="N/A"):
 
     for guide_rna in guide_rnas:
         # click.echo(guide_rna)
@@ -91,7 +94,7 @@ def write_guide_rnas(guide_rnas, output_file, input_id="N/A"):
                     guide_rna["target"],
                     str(guide_rna["pam"]),
                     str(guide_rna["pred"]),
-                    input_id,
+                    seq_id,
                 ]
             ),
             file=output_file,