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Commit 6e0f498b authored by Nicolas MAILLET's avatar Nicolas MAILLET
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change -i to -s in user guide when needed

parent dbc48a66
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        docs/userguide.rst
        View file @ 6e0f498b
        ......@@ -194,7 +194,7 @@ Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after
        .. code-block:: none
        $ rpg -i PKPKPKPK -e 28 29
        $ rpg -s PKPKPKPK -e 28 29
        >Input_0_afterP_1_1_115.13198_5.54
        P
        >Input_1_afterP_3_2_243.30608_9.4
        ......@@ -214,7 +214,7 @@ Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the follow
        .. code-block:: none
        $ rpg -i PKPKPKPK -e 28 29 -d c
        $ rpg -s PKPKPKPK -e 28 29 -d c
        >Input_0_afterP-afterK_1_1_115.13198_5.54
        P
        >Input_1_afterP-afterK_2_1_146.18938_9.4
        ......@@ -248,7 +248,7 @@ For example, using:
        .. code-block:: none
        rpg -i QWSDORESDF -e 1 2 3 -m 1.4 2.6
        rpg -s 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.
        ......@@ -317,7 +317,7 @@ With default verbosity level (no **-v** nor **-q** option), the output is:
        .. code-block:: none
        $ rpg -i QWSDORESDF -e 1
        $ rpg -s QWSDORESDF -e 1
        >Input_0_Asp-N_3_3_419.43738_5.54
        QWS
        >Input_1_Asp-N_8_5_742.78688_4.16
        ......@@ -329,7 +329,7 @@ Increasing verbosity by one, *i.e.* using **-v**, adds information about used op
        .. code-block:: none
        $ rpg -i QWSDORESDF -e 1 -v
        $ rpg -s QWSDORESDF -e 1 -v
        Warning: File 'peptides.fasta' already exit!
        Overwrite it? (y/n)
        y
        ......@@ -349,7 +349,7 @@ Increasing verbosity by two, *i.e.* using **-vv**, also adds statistics about ea
        .. code-block:: none
        $ rpg -i QWSDORESDF -e 1 -vv
        $ rpg -s QWSDORESDF -e 1 -vv
        Warning: File 'peptides.fasta' already exit!
        Overwrite it? (y/n)
        y
        ......@@ -378,7 +378,7 @@ Decreasing verbosity, *i.e.* using **-q** option, removes all information but er
        .. code-block:: none
        $ rpg -i QWSDORESDF -e 1 -q
        $ rpg -s QWSDORESDF -e 1 -q
        Warning: File 'peptides.fasta' already exit!
        Overwrite it? (y/n)
        y
        ......@@ -443,13 +443,13 @@ Note that this enzyme will only cleave if it finds the motif C*BAD, where * coul
        Add another enzyme? (y/n)
        n
        $ rpg -i CWBADE -e 43
        $ rpg -s CWBADE -e 43
        >Input_0_rpg_example_userguide_3_3_307.36728_5.46
        CWB
        >Input_1_rpg_example_userguide_6_3_333.29818_3.4
        ADE
        $ rpg -i FAD -e 43
        $ rpg -s FAD -e 43
        >Input_0_rpg_example_userguide_0_3_351.35928_3.6
        FAD
        ......@@ -482,19 +482,19 @@ It is important to note that for each enzyme, it is enough that one of the rule
        Add another enzyme? (y/n)
        n
        $ rpg -i CWBADE -e 43
        $ rpg -s CWBADE -e 43
        >Input_0_rpg_example_userguide_3_3_307.36728_5.46
        CWB
        >Input_1_rpg_example_userguide_6_3_333.29818_3.4
        ADE
        $ rpg -i FAD -e 43
        $ rpg -s FAD -e 43
        >Input_0_rpg_example_userguide_1_1_165.19188_5.54
        F
        >Input_1_rpg_example_userguide_3_2_204.18268_3.6
        AD
        $ rpg -i BAD -e 43
        $ rpg -s BAD -e 43
        >Input_0_rpg_example_userguide_0_3_204.18268_3.6
        BAD
        ......@@ -576,13 +576,13 @@ This enzyme will always cleave before A when not followed by P:
        Add another enzyme? (y/n)
        n
        rpg -i CWBADE -e 43
        rpg -s CWBADE -e 43
        >Input_0_rpg_example_userguide_3_3_307.36728_5.46
        CWB
        >Input_1_rpg_example_userguide_6_3_333.29818_3.4
        ADE
        rpg -i CWBAPE -e 43
        rpg -s CWBAPE -e 43
        >Input_0_rpg_example_userguide_0_6_604.67828_3.6
        CWBAPE
        ......@@ -616,25 +616,25 @@ This enzyme will always cleave before A (`P1'` ) when not followed by P (`P2'` )
        Add another enzyme? (y/n)
        n
        rpg -i CWBADE -e 43
        rpg -s CWBADE -e 43
        >Input_0_rpg_example_userguide_3_3_307.36728_5.46
        CWB
        >Input_1_rpg_example_userguide_6_3_333.29818_3.4
        ADE
        rpg -i CWBAPE -e 43
        rpg -s CWBAPE -e 43
        >Input_0_rpg_example_userguide_0_6_604.67828_3.6
        CWBAPE
        rpg -i GTBAMF -e 43
        rpg -s GTBAMF -e 43
        >Input_0_rpg_example_userguide_0_6_525.62028_5.54
        GTBAMF
        rpg -i GTBAPE -e 43
        rpg -s GTBAPE -e 43
        >Input_0_rpg_example_userguide_0_6_473.48328_3.6
        GTBAPE
        rpg -i GTBAME -e 43
        rpg -s GTBAME -e 43
        >Input_0_rpg_example_userguide_3_3_176.17228_5.54
        GTB
        >Input_1_rpg_example_userguide_6_3_349.40218_3.6
        ......
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