<commit_before>karinlag_utils
==============

Repository for HTS utility scripts


<commit_msg>Added script description to readme<commit_after>karinlag_utils
==============

Repository for HTS utility scripts

Contents:

same_mid_quantitate.py

Purpose: detect,trim and quantify MID tags in both ends of 454 sequences.

Options:

Options:
  -h, --help            show this help message and exit
  -f FILE, --fastafile=FILE
                        fasta filename
  -q FILE, --qualfile=FILE
                        qual file, optional
  -m FILE, --midfile=FILE
                        midfile name
  -v INT, --varsize=INT
                        variable region size
  -o STRING, --outnametag=STRING
                        output filename tag

This script takes as input a fasta file, and optionally a qual file, together with a file listing MID tag names and sequences. The script goes through each sequence and tries to find any of the listed tags in either end of the sequence (in the 3´ end, the reverse complement is searched for). The tag should be found within the set variable size (-v) in either end, otherwise it is not considered as found. If a tag is found (in either end) within the varsize limit, any trailing characters are removed, and the sequenced is output with the tag name(s) added to the fasta/qual description line. Note: a sequence will be included in the output only if a forward MID is found. Additionally, the sequence should in the end either have the same mid reverse complemented, or no mid should be found. 




{'fraction_non_alphanumeric': 0.06294613887086307, 'fraction_numerical': 0.0025957170668397143, 'mean_word_length': 2.8646616541353382, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7330212', 'n_tokens_mistral': 393, 'n_tokens_neox': 370, 'n_words': 211}