Gregory W. Schwartz
This program will take a fasta file, do certain filterings and transformations as specified by the user, and return the new fasta file.
stack install
The recommended usage for this program is to pipe in a fasta stream and make only one transformation at a time (not necessary, but the ordering can get confusing so to minimize assumptions about the ordering it's best to do it in the order you request). For instance, to translate the sequences:
cat input.fasta | modify-fasta -u Nucleotides --convert-to-amino-acids > output.fasta
To trim trailing nucleotides:
cat input.fasta | modify-fasta -u Nucleotides --trim-frame > output.fasta
To only return MOUSE entries (where the entry header looks like
"acc15|inframe|3|MOUSE|False") and cut off the amino acids after position 20:
cat input.fasta | modify-fasta -u AminoAcid --input-custom-filter "(4, ^MOUSE$)" | modify-fasta -u AminoAcid --stop 20 > output.fasta
To use the mutation based arguments, make sure that the fasta file is in CLIP format:
>>Germline1\ngermlinesequence\n>Somatic1\nsomaticsequence\n>Somatic2\nsomaticsequence\n>>Germline2\ngermlinesequence\n etc.
To only include codons with over 0 silent mutations (replacement mutation
containing codons would be replaced with ---):
cat input_clip.fasta | modify-fasta -u Nucleotide --clip-fasta --input-mut-type "Silent" --input-codon-mut 0 --input-codon-mut-type ">"
modify-fasta, Gregory W. Schwartz
Usage: modify-fasta [-i|--input FILE] (-u|--unit AminoAcid|Nucleotide)
[-L|--legacy] [-A|--clip-fasta]
[-C|--convert-to-amino-acids]
[-F|--fill-in (FIELD, START, 'CHARACTER')]
[-t|--start [ ] | INT] [-p|--stop [ ] | INT]
[--frequent-mutation-min [ ] | INT]
[--frequent-mutation-count [ ] | INT]
[--frequent-mutation-percent [ ] | PERCENT]
[-l|--add-length] [-N|--remove-N] [-g|--remove-germlines]
[-h|--remove-highly-mutated] [-s|--remove-stops]
[-d|--legacy-remove-duplicates] [-O|--remove-out-of-frame]
[-Y|--remove-unknown-nucleotides]
[--input-inframe [ ] | FIELD] [--input-outframe [ ] | FIELD]
[-y|--trim-frame] [-r|--input-stop-range [106]|INT]
[-c|--input-codon-mut [-1]|0|1|2|3]
[-T|--input-codon-mut-type [=]|>|<]
[-M|--input-mut-type [All]|Silent|Replacement]
[-e|--input-change-field ((FIELD (Int), VALUE (String))]
[-f|--input-custom-filter ((FIELD (Int), VALUE (String))]
[-G|--legacy-custom-germline] [-m|--custom-remove]
[-V|--legacy-gene-allele-field [1]|INT] [-v|--legacy-count]
[-o|--output FILE]
Modify fasta (and CLIP) files in several optional ways. Order of
transformation goes: seqInFrame -> customFilter -> noStops ->
removeHighMutations -> getMutations -> getFrequentMutations -> cutSequence ->
fillIn -> noNs -> changeHeader -> ntToaa -> includeLength, so if you require a
different order (which can change results dramatically), then do so one at a
time through the wonderful world of piping.
Available options:
-h,--help Show this help text
-i,--input FILE The input fasta file or CLIP fasta file
-u,--unit AminoAcid|Nucleotide
Whether these sequences are composed of amino acids
(AminoAcid) or nucleotides (Nucleotide)
-L,--legacy Whether to use the legacy version with no pipes.
Note: The legacy version supports more features but
is greedy in terms of speed and memory. Use only if
really needed. Features that are legacy only are
noted in this documentation
-A,--clip-fasta Whether the input is a clip fasta file (has germline
>> sequences).
-C,--convert-to-amino-acids
Whether to convert the filtered sequences to amino
acids in the output. Applied last, even after add
length.
-F,--fill-in (FIELD, START, 'CHARACTER')
Use the FIELD index (1 indexed, split by '|') in the
header to fill in the unknown character CHARACTER
with the respective character in that field. Use the
START value to let the program know where the string
in the field starts from in the sequence. For
instance, a header of >H2O|HELLO for the sequence
HIMANHELXODUDE and a value of fill-in of (2, 6, 'X')
would change the sequence to HIMANHELLODUDE. If the
string in the field has the unknown character as
well, i.e. >H2O|HELXO, then the sequence is
considered bad and is removed
-t,--start [ ] | INT Remove everything before this position (1 indexed).
Done first just after filtering.
-p,--stop [ ] | INT Remove everything after this position (1 indexed).
Done first just after filtering.
--frequent-mutation-min [ ] | INT
Minimum number of sequences required for a clone to
be valid in the calculation of frequent mutations,
replaces with gaps otherwise
--frequent-mutation-count [ ] | INT
Only include codons containing a mutation present in
this many sequences in the clone or more. 0 is all
sequences. Converts the unincluded codons to gaps.
--frequent-mutation-percent [ ] | PERCENT
Only include codons containing a mutation present in
this percentage of sequences in the clone or more. 0
is all sequences. Converts the unincluded codons to
gaps.
-l,--add-length Whether to append the length of the sequence to the
end of the header, calculated after
--convert-to-amino-acids if enabled
-N,--remove-N Whether to replace N or n in the sequence with a gap,
'-'
-g,--remove-germlines Whether to remove germlines.
-h,--remove-highly-mutated
Whether to remove highly mutated clone sequences (a
third of their sequence are different amino acids).
-s,--remove-stops Whether to remove sequences with stop codons
-d,--legacy-remove-duplicates
Whether to remove duplicate sequences. LEGACY ONLY
-O,--remove-out-of-frame Whether to remove sequences that are out of frame--if
the sequences or number of gaps is not divisible by 3
-Y,--remove-unknown-nucleotides
Convert unknown nucleotides (not ACGTN-.) to gaps (-)
--input-inframe [ ] | FIELD
Represents the 1 indexed field split by '|'
containing the inframe value (frames are 0, 1, or 2
like USCS definitions). For use with trim-frame.
--input-outframe [ ] | FIELD
Represents the 1 indexed field split by '|'
containing the outframe value (frames are 0, 1, or 2
like USCS definitions). For use with trim-frame.
-y,--trim-frame Trim each sequence to be in frame by remove extra
nucleotides at the end. If input-inframe or
input-outframe is specified, follow those rules
instead.
-r,--input-stop-range [106]|INT
Only search for stops with remove-stops up to this
amino acid position
-c,--input-codon-mut [-1]|0|1|2|3
Only include codons with this many mutations or less
or more, depending on input-codon-mut-type (-1 is the
same as include all codons). Converts the unincluded
codon to gaps.
-T,--input-codon-mut-type [=]|>|<
Only include codons with this many mutations (=) (or
lesser (<) or greater (>), depending on
input-codon-mut). Converts the unincluded codon to
gaps.
-M,--input-mut-type [All]|Silent|Replacement
Only include codons with this all mutations (All),
(or silent (Silent) or replacement (Replacement)).
-e,--input-change-field ((FIELD (Int), VALUE (String))
Change a field to a match, so a regex "ch.*_" to
field 2 of ">abc|brie_cheese_dude" would result in
">abc|cheese_". Useful for getting specific
properties from a field. Can take a list of format
"(Int, String)&&(Int, String)&& ..." and so on. The
String is in regex format (POSIX extended). The first
in the tuple is the location of the field (1 indexed,
split by '|').
-f,--input-custom-filter ((FIELD (Int), VALUE (String))
A custom filter. Can take a list of format "(Int,
String)&&(Int, String)&& ..." and so on. The String
is in regex format (POSIX extended), so if the entire
string 'a' is in the whole field, then you need to
input '^a$' for the beginning to the end! The first
in the tuple is the location of the field (1 indexed,
split by '|'). If you want to apply to the entire
header, either have the location as 0 or exclude the
location altogether (, Day 3|IGHV3) for instance will
match if the entire header is '>Day 3|IGHV3'. This
list will be filtered one at a time, so you cannot
get multiple filters, but you can remove multiple
filters.
-G,--legacy-custom-germline
Whether to apply the custom filter to germlines (>>)
instead of sequences (>). LEGACY ONLY
-m,--custom-remove Whether to remove the sequences containing the custom
filter as opposed to remove the sequences that don't
contain the filter
-V,--legacy-gene-allele-field [1]|INT
The field (1 indexed) of the gene allele name. LEGACY
ONLY
-v,--legacy-count Do not save output, just count genes and alleles from
the results. Requires gene-allele-field. LEGACY ONLY
-o,--output FILE The output fasta file