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Top Forums Shell Programming and Scripting Bash to create sub directories from specific file extension Post 303032560 by nezabudka on Wednesday 20th of March 2019 11:44:06 AM
Old 03-20-2019
Code:
$(find * -type f -name "*.bam" | cut -d_ -f2 | cut -d. -f1)

--- Post updated at 18:32 ---

endless running through directories means only one thing, you don't know where you will when will creating catalogs
Code:
find "$RDIR"/BAM -type f -name "*.bam" | cut -d_ -f2 | cut -d. -f1 |  xargs -I {} mkdir -p "$RDIR/"{}

--- Post updated at 18:44 ---

In any case, it is better not to run on items twice.
Code:
do
    cd "$RDIR"/BAM
    find * -type f -name "*.bam" | cut -d_ -f2 | cut -d. -f1 |  xargs -I {} mkdir -p "$RDIR/"{}
done


Last edited by nezabudka; 03-20-2019 at 12:37 PM..
 

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cut(1)								   User Commands							    cut(1)

NAME
cut - cut out selected fields of each line of a file SYNOPSIS
cut -b list [-n] [file]... cut -c list [file]... cut -f list [-d delim] [-s] [file]... DESCRIPTION
Use the cut utility to cut out columns from a table or fields from each line of a file; in data base parlance, it implements the projection of a relation. The fields as specified by list can be fixed length, that is, character positions as on a punched card (-c option) or the length can vary from line to line and be marked with a field delimiter character like TAB (-f option). cut can be used as a filter. Either the -b, -c, or -f option must be specified. Use grep(1) to make horizontal ``cuts'' (by context) through a file, or paste(1) to put files together column-wise (that is, horizontally). To reorder columns in a table, use cut and paste. OPTIONS
The following options are supported: list A comma-separated or blank-character-separated list of integer field numbers (in increasing order), with optional - to indi- cate ranges (for instance, 1,4,7; 1-3,8; -5,10 (short for 1-5,10); or 3- (short for third through last field)). -b list The list following -b specifies byte positions (for instance, -b1-72 would pass the first 72 bytes of each line). When -b and -n are used together, list is adjusted so that no multi-byte character is split. -c list The list following -c specifies character positions (for instance, -c1-72 would pass the first 72 characters of each line). -d delim The character following -d is the field delimiter (-f option only). Default is tab. Space or other characters with special meaning to the shell must be quoted. delim can be a multi-byte character. -f list The list following -f is a list of fields assumed to be separated in the file by a delimiter character (see -d ); for instance, -f1,7 copies the first and seventh field only. Lines with no field delimiters will be passed through intact (useful for table subheadings), unless -s is specified. -n Do not split characters. When -b list and -n are used together, list is adjusted so that no multi-byte character is split. -s Suppresses lines with no delimiter characters in case of -f option. Unless specified, lines with no delimiters will be passed through untouched. OPERANDS
The following operands are supported: file A path name of an input file. If no file operands are specified, or if a file operand is -, the standard input will be used. USAGE
See largefile(5) for the description of the behavior of cut when encountering files greater than or equal to 2 Gbyte (2^31 bytes). EXAMPLES
Example 1 Mapping user IDs A mapping of user IDs to names follows: example% cut -d: -f1,5 /etc/passwd Example 2 Setting current login name To set name to current login name: example$ name=`who am i | cut -f1 -d' '` ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of cut: LANG, LC_ALL, LC_CTYPE, LC_MES- SAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 All input files were output successfully. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWcsu | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
grep(1), paste(1), attributes(5), environ(5), largefile(5), standards(5) DIAGNOSTICS
cut: -n may only be used with -b cut: -d may only be used with -f cut: -s may only be used with -f cut: cannot open <file> Either file cannot be read or does not exist. If multiple files are present, processing continues. cut: no delimiter specified Missing delim on -d option. cut: invalid delimiter cut: no list specified Missing list on -b, -c, or -f option. cut: invalid range specifier cut: too many ranges specified cut: range must be increasing cut: invalid character in range cut: internal error processing input cut: invalid multibyte character cut: unable to allocate enough memory SunOS 5.11 29 Apr 1999 cut(1)
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